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- PDB-7rea: Apo Hemophilin from A. baumannii -

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Basic information

Entry
Database: PDB / ID: 7rea
TitleApo Hemophilin from A. baumannii
ComponentsHemophilin
KeywordsMETAL TRANSPORT / Heme Binding / Secreted
Function / homologyOuter membrane protein/outer membrane enzyme PagP, beta-barrel / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii NIPH 201 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBateman, T.J. / Shah, M. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115182 Canada
CitationJournal: Nat Commun / Year: 2021
Title: A Slam-dependent hemophore contributes to heme acquisition in the bacterial pathogen Acinetobacter baumannii.
Authors: Bateman, T.J. / Shah, M. / Ho, T.P. / Shin, H.E. / Pan, C. / Harris, G. / Fegan, J.E. / Islam, E.A. / Ahn, S.K. / Hooda, Y. / Gray-Owen, S.D. / Chen, W. / Moraes, T.F.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemophilin


Theoretical massNumber of molelcules
Total (without water)25,1281
Polymers25,1281
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.260, 68.480, 71.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemophilin


Mass: 25128.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii NIPH 201 (bacteria)
Gene: F922_02812 / Production host: Escherichia coli (E. coli) / References: UniProt: N9GH75
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 30% (w/v) PEG8K, 0.1M sodium acetate pH 4.5, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 19, 2016
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.49→37.57 Å / Num. obs: 35995 / % possible obs: 99.99 % / Redundancy: 14 % / CC1/2: 0.999 / Net I/σ(I): 17.43
Reflection shellResolution: 1.49→1.53 Å / Num. unique obs: 3549 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RED

7red


Resolution: 1.49→37.566 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1673 1800 5 %
Rwork0.1461 34195 -
obs0.1472 35995 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.76 Å2 / Biso mean: 12.2915 Å2 / Biso min: 3.69 Å2
Refinement stepCycle: final / Resolution: 1.49→37.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 0 322 2013
Biso mean---25.12 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.49-1.53030.20181360.18462587
1.5303-1.57530.20081370.15672597
1.5753-1.62620.18131350.15292578
1.6262-1.68430.19031350.14752564
1.6843-1.75170.17871380.15032620
1.7517-1.83140.17571370.14392605
1.8314-1.9280.18341390.14182629
1.928-2.04880.16341360.13742598
2.0488-2.2070.16721390.1372638
2.207-2.4290.16841380.14992620
2.429-2.78040.17691400.15112667
2.7804-3.50260.151410.14162679
3.5026-37.5660.14581490.14282813
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.91361.46560.82621.60480.91342.5967-0.13670.33440.4118-0.17890.1670.1205-0.2201-0.02610.00380.079-0.0008-0.01510.05890.01960.1308-11.45496.15279.4748
23.68120.44740.26462.57970.40062.4198-0.0386-0.15690.10540.13130.01230.1321-0.3328-0.12330.01230.13870.01430.00790.0488-0.00110.0948-10.661310.222319.0372
31.8420.498-1.15292.14141.061.66160.04950.04010.2870.01790.03230.2204-0.3641-0.2434-0.07090.11620.03040.01650.0999-0.00550.1114-14.87534.791223.4599
42.95442.95463.12914.24492.99123.3292-0.0282-0.7839-0.29630.4353-0.10760.42410.2553-0.49190.12720.13120.02060.0150.14180.02710.1175-17.9249-6.356332.0366
55.1877-2.0896-2.58271.3921.23441.907-0.16-0.1101-0.1240.09460.05620.04530.141-0.01030.1020.07-0.0082-0.0060.0457-0.00020.0554-13.2176-7.348823.7593
65.78840.31030.26411.1243-0.16241.2063-0.0366-0.03770.06040.06350.02930.0048-0.0158-0.00140.00170.04730.0056-0.00430.0303-0.01430.0274-9.5849-2.351518.2501
77.9431.4935-2.76386.33733.63075.8138-0.06-0.00730.001-0.1266-0.10770.2084-0.0544-0.35240.16110.0468-0.0148-0.01510.1238-0.00870.0775-24.6409-5.772312.8399
81.4701-0.1438-0.32710.65670.04290.86870.0005-0.08730.062-0.0125-0.0094-0.02240.02190.0430.01150.04410.001-0.00890.0436-0.00310.0253-2.9938-5.17710.8086
96.48463.4685-1.11292.4427-0.4960.357-0.06290.0275-0.1442-0.07130.0149-0.06420.0832-0.01440.04960.07850.00880.0010.0419-0.00220.0386-1.0162-12.15244.2367
107.9346.84830.71768.73030.68351.7007-0.17870.20610.1772-0.21070.17320.2090.02560.0855-0.0070.04860.020.00920.0288-0.00550.03281.276-4.8993-0.8671
111.49690.90060.09111.63660.08591.0919-0.0496-0.01580.0352-0.11530.04760.02250.1063-0.01460.00330.04810.0081-0.00640.0405-0.00260.0448-4.3218-5.54963.4026
123.6002-0.18212.11891.4930.23582.6717-0.11460.04490.1692-0.10510.00180.0853-0.0009-0.06040.11160.0511-0.01640.00660.02340.00350.0321-9.6204-8.19446.1528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2(chain A and resid 21:44)A21 - 44
2X-RAY DIFFRACTION3(chain A and resid 45:59)A45 - 59
3X-RAY DIFFRACTION4(chain A and resid 60:65)A60 - 65
4X-RAY DIFFRACTION5(chain A and resid 66:95)A66 - 95
5X-RAY DIFFRACTION6(chain A and resid 96:114)A96 - 114
6X-RAY DIFFRACTION7(chain A and resid 115:122)A115 - 122
7X-RAY DIFFRACTION8(chain A and resid 123:164)A123 - 164
8X-RAY DIFFRACTION9(chain A and resid 165:186)A165 - 186
9X-RAY DIFFRACTION10(chain A and resid 187:197)A187 - 197
10X-RAY DIFFRACTION11(chain A and resid 198:235)A198 - 235
11X-RAY DIFFRACTION12(chain A and resid 236:251)A236 - 251

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